The 2D clone wars series is in kind of a weird place in that it's clearly not canon, and yet certain events depicted within it still *happened* more or less as they did on the show (allowing for it's highly bombastic OTT stylistic interpretation of course.)
The one that's probably shown up the most at this point in the Jedi Knighting ceremony. While we've never seen a canon version of Anakin's Knighting, every other one we've seen since has been patterned direction on that version.
Another fairly minor but logical one is how Artoo & Threepio changed owners between AotC & RotS; they were essentially exchanged as wedding gifts.
Some of that is likely due to some notes exchanged between the Clone Wars multimedia project (that including not just the animated show, but the tie-in books and comics as well) and the movie production people, some may simply be because some of the same people worked on both 2D and animated versions, and a good idea is a good idea.
Indeed the 3D show seemed to deliberately avoid retreading the same ground as the microseries, so some of those elements (like Ventress's recruitment) just got left in by default.
Speaking of which; I feel I should clarify that so far as I know Ventress, was not created specifically for the animated show as is often claimed. Both she and Durge were developed as part of the aforementioned clone wars multi-media project coordinated by LF licencing. Hence all of the related comics and novels coming out around the same time.
There's even a fun little connection there with 'Force Unleashed': The comics writer assigned to develop her character initially named her 'Juno Eclipse', but that was decided to not sound villainous enough (I think Leland Chee suggested the
'Throne of Blood' reference?) Said writer later worked on Force Unleased and re-used the rejected name for the love interest character.
